- Research article
- Open Access
Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots
- Maria E Morán-Diez†1, 4,
- Naomi Trushina†2,
- Netta Li Lamdan2,
- Lea Rosenfelder2,
- Prasun K Mukherjee3,
- Charles M Kenerley1 and
- Benjamin A Horwitz2Email author
© Morán-Diez et al.; licensee Biomed Central. 2015
- Received: 9 June 2014
- Accepted: 30 December 2014
- Published: 22 January 2015
Members of the fungal genus Trichoderma directly antagonize soil-borne fungal pathogens, and an increasing number of species are studied for their potential in biocontrol of plant pathogens in agriculture. Some species also colonize plant roots, promoting systemic resistance. The Trichoderma-root interaction is hosted by a wide range of plant species, including monocots and dicots.
To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on microarrays of 11645 unique oligonucleotides designed from the predicted protein-coding gene models. Transcript levels of 210 genes were modulated by interaction with roots. Almost all were up-regulated. Glycoside hydrolases and transporters were highly represented among transcripts induced by co-culture with roots. Of the genes up-regulated on either or both host plants, 35 differed significantly in their expression levels between maize and tomato. Ten of these were expressed higher in the fungus in co-culture with tomato roots than with maize. Average transcript levels for these genes ranged from 1.9 fold higher on tomato than on maize to 60.9 fold for the most tomato-specific gene. The other 25 host-specific transcripts were expressed more strongly in co-culture with maize than with tomato. Average transcript levels for these genes were 2.5 to 196 fold higher on maize than on tomato.
Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner. The differentially expressed genes encode proteins belonging to several functional classes including enzymes, transporters and small secreted proteins. Among them, glycoside hydrolases and transporters are highlighted by their abundance and suggest an important factor in the metabolism of host cell walls during colonization of the outer root layers. Host-specific gene expression may contribute to the ability of T. virens to colonize the roots of a wide range of plant species.
- Glycoside Hydrolase
- Glycoside Hydrolase Family
- Hydroponic Culture
- Tomato Root
- Host Cell Wall
Some members of the genus Trichoderma, including T. virens, T. harzianum, T. asperellum and T. atroviride, are employed as biocontrol agents of plant pathogens worldwide. These soil fungi are keen mycoparasites, generally rhizosphere competent, and some have the ability to extensively colonize the outer root layers [1-4]. In addition to direct parasitism of plant pathogens, interactions with Trichoderma enhance plant fitness in response to biotic and abiotic stresses [5,6]. Benefits derived by the host include: a) increased plant growth [7-11], (b) increased resistance to abiotic stresses such as drought and salinity [12-16], (c) induced host defense responses to pathogens [17-23]; (d) enhanced nutrient uptake and fertilizer use efficiency [16,24-26], and (e) increased photosynthetic rates [27,28]. A recent microarray study of two dicots showed that in the plant, genes related to tolerance of oxidative and osmotic stresses are induced by the Trichoderma-plant interaction . Growth promotion of bean plants has been found to be strain-specific . The combination of close interaction with plants and the ability to tolerate heavy metals make some strains of T. harzianum  and T. virens  effective agents for soil bioremediation and plant growth promotion.
The Trichoderma-plant interaction has been defined as an opportunistic symbiosis . The T. asperellum – cucumber interaction was followed by electron microscopy, and growth is extracellular, with hyphae penetrating the outer root cortex . The interaction between T. harzianum and tomato roots was observed by confocal microscopy with a GFP-expressing strain . In hydroponic cultures during early colonization (10 hours), hyphae were observed growing between plant cell walls, and by 24 h, the root surface was extensively colonized. In soil, a switch to yeast-like morphology was observed following colonization. The fungus, after 48 hours, was mainly extracellular although occasionally intracellular, and in these cases the colonized cell appears to remain viable. After longer times of interaction in soil (72 hours) the fungus produced yeast-like cells .
In the T. virens – maize interaction, GFP-expressing hyphae are observed on the root surface and growing between cell walls in the epidermis and outer cortex, with no evidence of intracellular growth . The Trichoderma-root interaction is not identical to any other previously studied symbiosis, but the interaction is reminiscent in some ways of ectomycorrhizae (EM). Images of Trichoderma spp. colonizing maize  or tomato roots  show the colonizing mycelia as a loose and relatively sparse network, which is less sharply delineated than the massive EM mantle . In both symbioses, mycelia penetrate the root apoplast, but it is not clear how similar are the distributions within the root. The ectomycorrhizal fungus Laccaria bicolor secretes a small protein (MiSSP7), highly expressed during colonization of tree roots and needed to establish the symbiosis [37,38]. MiSSP7 is imported into plant cells where it interacts with a transcriptional repressor to antagonize jasmonate-induced gene expression . In arbuscular mycorrhizae, a plant nucleus-targeted effector counteracts the immune response by interacting with a specific plant transcription factor, allowing establishment of the biotrophic interaction . Piriformospora indica, like Trichoderma virens, has a wide host range, interacting with roots of monocots and dicots. A recent transcriptomic study showed that this basidiomycete root endophyte tailors the expression of its genome to the host plant and to the stage of the mutualistic interaction .
The genomes of the cellulose degrader T. reesei and two mycotrophic, plant-interacting species, T. atroviride and T. virens, have been published [42,43]. The sequences have provided the tools for a genome-wide view of Trichoderma-fungal and Trichoderma-plant interactions [44,45]. Several studies have addressed the transcriptome of different Trichoderma species, in interaction with a particular plant host [35,46-48]. Studies of Trichoderma transcriptomes in interaction with plant roots, using arrays designed from Trichoderma ESTs, showed regulation of genes related to redox reactions, transport, lipid metabolism and detoxification ; small secreted and cell surface proteins, proteases, endochitinase ECH42, and novel genes that could be related to nitric oxide biosynthesis, xenobiotic detoxification, and development ; and a predominance of carbohydrate metabolism-genes . These studies, which indicate that interaction with the plant host programs expression of many genes in the fungal partner, employed several Trichoderma species and times of interaction with the plant host. Here, we compared the same Trichoderma strain in interaction with two host plants under the same conditions, to identify host-specific transcriptomic signatures.
Although the Trichoderma-root interaction represents a distinct type of symbiosis, the similarities to other fungal-plant symbioses led us to the working hypotheses that (1) the fungal transcriptome should depend on the host plant species, providing a molecular basis for the wide host range; and, (2) small secreted proteins (SSPs) and other secreted proteins may be important for the mutualistic interaction and for induction of disease resistance in colonized plants. In this study we used oligonucleotide microarrays designed from the predicted protein-encoding gene models of T. virens  to ask what genes are up-regulated at the transcriptional level, comparing the interaction with either tomato or maize roots. The results of comparing two plant hosts, monocot and dicot, under the same growth conditions suggest that a different repertoire of genes is expressed in response to different hosts and provide us with a better understanding of this interaction. Such studies would be helpful for crop-specific application of T. virens for maximizing the benefits derived from this type of plant-microbe interactions. This study would also be helpful in isolating novel promoters for driving expression of desirable Trichoderma genes (e.g., elicitors) in the rhizosphere-competent species.
Bioassay: seedling and fungal culture
For plant interactions, maize seeds (Silver Queen hybrid) were treated with 70% ethanol for 5 min, rinsed with water, soaked in 10% hydrogen peroxide solution for 2 hours, rinsed with water, and germinated on moist sterile filter papers to screen for contamination (procedure modified from: Djonovic et al., ). After four to five days incubation at 27°C, five seedlings of similar root length were selected and placed on plastic screens suspended in jars containing 250 ml of half strength Murashige and Skoog (MS medium) with vitamins and 0.05% sucrose. The seedlings were grown in a temperature-controlled growth room under fluorescent light (cool white and cool daylight tubes in alternating positions, 120–150 μmol m−2 s−1) (16:8 hours, day:night) for three days at 23-25°C. Tomato seedlings were prepared by treating seeds (cultivar Moneymaker) with 70% ethanol for 20 min, rinsing with water, soaking in 10% bleach solution for 5 min, rinsing in water, and germinated on MS supplemented with 0.8% agar. After seven days, five seedlings of same root length were selected for placing in the hydroponic system.
Sample collection and RNA preparation
Four treatments, with three biological replicates per treatment, were collected: maize roots with T. virens (M + Tv); tomato roots with T. virens (T + Tv); maize or tomato roots without fungus (M-C or T-C, respectively); and T. virens without plant roots (Tv). Root systems from the same jar were harvested as an individual sample after 72 hours root-fungus interaction. Samples were gently washed with distilled water to remove clumps of fungal mycelia that adhered only loosely to the roots. The roots with remaining fungal mycelia were excised from the seedlings, frozen in liquid nitrogen, and extracted directly or stored at −80°C. Control root samples without T. virens were grown and harvested as described above. For axenic culture, T. virens was grown under the same conditions in the hydroponic culture containers, but without plants.
Total RNA was extracted from 100 mg of ground tissue (fungus and/or roots) with TRI Reagent (Molecular Research Center, Cincinnati, OH) following the manufacturer’s instructions. The quality of the RNA extracts was evaluated using the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit (Agilent, Santa Clara, CA) according to the manufacturer’s instructions. Samples with electropherograms exhibiting sharp 18S and 28S rRNA peaks and showing no evidence of degradation were retained. The transcript of the T. virens histone H3 gene was easily detectable by RT-PCR in cDNA samples from T. virens and in interaction with maize or tomato, but not in control plant samples (data not shown).
Microarray conditions and analysis
Real time qPCR
Primer pairs used for qPCR amplification
Glycoside hydrolase family 7 protein
Secreted short-chain dehydrogenase/reductase
Secreted NAD-dependent epimerase/dehydratase
Small secreted cysteine rich
Class II hydrophobin
Polygalacturonase, glycoside hydrolase family 28
Acetyl xylan esterase
Secreted short-chain dehydrogenase/reductase
Xylanase, glycoside hydrolase family 10
Reporter gene construct
We chose the CBH1 glycoside hydrolase gene (Protein ID: 90504; http://genome.jgi-psf.org/TriviGv29_8_2/TriviGv29_8_2.home.html) because the transcript is abundant in samples from root cultures inoculated with T. virens. Furthermore, this gene was strongly induced in interaction of T. virens with tomato roots in an earlier study . This suggested that the upstream region includes strong expression signals that could be used to design a construct to report gene expression in response to Trichoderma-root interactions. A 2510 bp region upstream of the predicted translation start was amplified from T. virens G29.8 genomic DNA, using the forward primer P90504f, GTAGAACTGAAAAGCTTCGGTCAATC and reverse primer P90504r, CAATTTCTGATCCATGGTGTACAATCTTTG. The forward primer contains two mismatches, creating a HindIII site. The reverse primer contains two mismatches, converting the ATG start codon into a NcoI site. The product was cloned into pTZ57R/T (InsTAclone, Thermo Scientific) to obtain plasmid p90504. A 960 bp NcoI/SalI fragment from gGFP (, Fungal Genetics Stock Center) containing the GFP coding sequence was ligated (T4 DNA ligase, Fermentas) to p90504, which was digested with NcoI and SalI, and the ligation products transformed to E. coli HIT-DH5α (RBC Bioscience, Taiwan). Five μg of the resulting plasmid, p90504-GFP, were co-transformed together with 5 μg of pUCATPH (containing the hygromycin phosphotransferase hph gene with fungal expression signals ) to protoplasts of T. virens G29.8, using the PEG protocol as described by . After regeneration overnight, transformation plates were overlayed with 600 μg/ml hygromycin B (A.G. Scientific, San Diego, CA) in 1% agar (Difco). Colonies reaching the surface of the overlay were transferred to PDA (Difco) with 100 μg/ml hygromycin B. About 40 hygromycin-resistant colonies were screened by inoculating wells containing excised maize root sections in 0.5x MS medium with 0.05% sucrose. After three days incubation, the wells were observed under a binocular fluorescence microscope (Olympus). Three isolates that showed GFP expression were identified and one, designated C10, was used for experiments.
Microarray analysis of Trichoderma-root interactions
Genes regulated in interaction with both plant hosts
The expression of 14 T. virens genes was significantly up-regulated in interaction with both maize and tomato. Of these, 8 were found previously, in interaction with tomato (, coded by violet shading in Additional file 3: Table S2). A cluster of genes co-regulated in interaction with both host plants is shown in Figure 2B, annotated by JGI protein model ID number. Seven expression patterns of genes belonging to the set significantly up-regulated in both root interactions (Figure 2C) cluster together (indicated by yellow dots in Figure 2B). The 14 genes significantly up-regulated in interaction with both maize and tomato are mostly found on different scaffolds. In the two cases where a pair of genes was found on the same scaffold, the distance between them was very large (more than 600 kb). Similar expression patterns in the three conditions (Tv, M + Tv and T + Tv), as evident in Figure 2C, is therefore not reflected by co-localization in the genome. Ten of the 14 genes in this list are annotated as glycoside hydrolases. Seven of the eight genes found to be up-regulated by interaction with both maize and tomato in this study (sampled at 72 h) and with tomato (sampled at 20 h,  are annotated as glycoside hydrolases. The exception is ID 180068, encoding a protein with Zn finger and F-box domains, which might be have a regulatory function. Identification of glycoside hydrolase-encoding genes in experiments performed in different labs, and at a different sampling time, points to a core function: the ability to (partially) degrade the root cell walls.
Genes up-regulated in interaction with either or both plant hosts
Looking at the available annotations for the larger list of genes significantly up-regulated in interaction with either plant host, glycoside hydrolases are again prominent (Additional file 3: Table S2). Another class includes transporters (Additional file 3: Table S2, Figure 2D). There are several predicted transcription factors and other regulatory proteins, and some small secreted proteins. Two genes are related to iron acquisition: Fe permease FTR1 (ID 24347, v1.0; 195287, v2.0) and a ferric reductase (ID v1.0 11584, v2.0 147314). A similar picture, in general, was independently obtained by GO term analysis (Additional file 5: Figure S1). The highest-represented biological processes are polysaccharide catabolism, transmembrane transport, and oxidation-reduction (Additional file 5: Figure S1). An identical GO term analysis using a randomly chosen set of sequences (control, Additional file 5: Figure S1) resulted in a much more diverse representation of biological processes. Oxidation-reduction is also highly represented in the list obtained from the consensus annotation (see individual annotations in Additional file 3: Table S2), although this is not obvious in Figure 2D where oxidation-reduction is included in “metabolism”.
Different cell wall composition of the two plant hosts might be expected to play a role in the set of fungal genes expressed. The predicted substrates of the fungal glycoside hydrolase families represented (following  and the CAZy database, http://www.cazy.org/Glycoside-Hydrolases.html) do not appear, however, to be related in any direct way to the composition of maize vs tomato cell walls. As an example, we note that dicot walls are more pectin-rich than those of monocots . The endopolygalacturonase encoded by transcript 51095 is the unique member of family GH28 expressed in response to interaction with roots. If the product of 51095 is indeed the major induced pectin-degrading enzyme, one might have expected higher expression in tomato where the substrate is more abundant. This pattern was found  upon comparison of two Colletotrichum species. One species is a pathogen of Brassicaceae, and one of maize. C. higginsianum in the necrotrophic phase of its interaction with Arabidopsis was found to up-regulate a greater number of pectin-degrading enzyme genes than C. graminicola on maize . Our data show, however, up-regulation of the GH28 gene 51095 in interaction with both tomato and maize (Figure 3A, B). Dicot and grass cell walls both contain pectin, and the expression of enzyme genes will not always correspond directly with substrate levels. The predicted ortholog (E value 0.0, BLASTP) of 51095 in T. harzianum is ThPG1. Silencing of ThPG1 in T. harzianum showed that it is required for colonization of Arabidopsis roots . This could be tested for T. virens on tomato and maize. The question of how GH family expression might be related to host cell wall composition will need to be addressed at the protein, in addition to transcript, level. When and where each CAZyme is expressed in the root tissue is also important.
Genes differentially regulated in interaction with maize or tomato
Maize-specific expression of three genes, oxidoreductases 46185, 86039 and SSP 17705, was confirmed by qPCR (Figure 3). The intracellular invertase TvInv (ID v1.0 21923, v2.0 111987)  is specific to the maize interaction, though obviously one cannot exclude induction on tomato at a different time point from the 72 h sampled here. The tomato-specific up-regulated transcripts (Additional file 4: Table S3) remain to be further characterized.
The “cluster 3” SSP (ID 17705 v1.0/230434 v2.0) seems a promising candidate for functional analysis as a maize-interaction-specific small secreted protein.
Functional significance of regulated genes
The strong induction of genes for enzymes with the potential to degrade plant cell walls is interesting, as the interaction between T. virens and these two hosts is considered mutualistic. This finding is consistent with previous reports [46,47]. In the mutualistic interaction of barley with the basidiomycete Piriformospora indica –, hydrolytic enzymes and transporters are strongly induced following the transition from biotrophy to saprotrophic growth on dead root cortex cells. There is relatively little induction of these genes in the biotrophic P. indica-Arabidopsis interaction . While a full meta-analysis is beyond the scope of this study, the similarity between P. indica – barley and the T. virens interactions studied here suggests that the T. virens – root interactions have a limited necrotrophic aspect, like P. indica – barley and in contrast to P. indica - Arabidopsis. If so, cell death should be observed, and there is preliminary evidence for this from scattered propidium iodide staining of plant and fungal nuclei (Figure 4 and data not shown). Furthermore, this similarity between P. indica – barley and the two T. virens interactions points to parallel evolution of a mutualistic, ISR-promoting, fungal-root interaction distinct from mycorrhizae, in Basidiomycota and Ascomycota.
The genes identified here and in previous studies can provide specific reporters for the T. virens-root interaction. To test this concept we constructed a reporter in which GFP was expressed under control of the predicted upstream regulatory region from the 90504 gene. Transgenic lines expressing this construct showed strong GFP fluorescence in interaction with roots (Figure 4) and root sections (data not shown). The protein sequence of 90504, belonging to glycoside hydrolase (GH) family GH7, is nearly identical (three differences in amino acid sequence, all of which are similar) to the T. virens T87 gene CBHI (accession ACF93800) which is up-regulated in interaction with tomato . In hydroponic cultures, fluorescent hyphae could be detected in the outer root layers, while externally adhering hyphae showed fluorescence in or on some hyphal compartments (Figure 4). We have not confirmed penetration into root cortex cells under the conditions studied here, though GFP-expressing hyphae are closely associated with maize cells (Figure 4). Higher-resolution localization of T. virens hyphae in the root cortex will require a line expressing GFP at high, constitutive levels, like the T. harzianum line used in a recent study of the role of salicylic acid in limiting penetration into Arabidopsis roots . In the T. harzianum- tomato root interaction there is evidence for intracellular hyphae or yeast-like cells . If the T. virens – root interaction (at 3 days in hydroponic culture) most resembles the late-stage (14 days) P. indica- barley interaction, induction of hydrolytic enzymes might reflect saprotrophic on dead root cells. The majority of root cells at three days interaction, however, appear living, since their nuclei do not stain with propidium iodide (Figure 4B). The genome of the arbuscular mycorrhizal fungus Rhizophagus irregularis lacks GH families predicted to degrade plant cell wall polysaccharides . In contrast, these are induced in T. virens interacting with roots (for example, GH7, GH28, GH61). Two pectate lyase (GH28) genes are up-regulated in ectomycorrhiza, as is a GH61 gene (Suppl. Table 25 in: ). Visualization of the time course and location of expression of the GH genes during colonization should help to understand how T. virens fits into the biotroph – saprotroph – pathogen continuum.
Trichoderma spp. interact with both monocots and dicots. Different patterns of gene expression might facilitate this wide (and agriculturally beneficial) host range. In support of this view, we found that a number of genes were expressed specifically in response to either maize or tomato (Additional file 4: Table S3; Figures 6 and 7). One of these is invertase TvInv , expressed more than 100-fold higher on maize than on tomato. Several small secreted proteins are expressed preferentially in each interaction. Short-chain oxidoreductases appear to be characteristic of the maize interaction. Identification of the substrates of these predicted proteins, if they indeed have enzyme activity, might help identify their (specific) role in the Trichoderma-maize root interaction. In general, there are not enough functional data to fully understand why a particular set of genes is induced in the maize or tomato mutualism. The existence of specific reporters of each interaction, though, demonstrates specific transcriptomic signatures for the interaction with each plant.
This study provides a better knowledge of the crosstalk of Trichoderma virens, an agriculturally relevant biocontrol agent, with plants. Genes differentially expressed during interaction with plant roots encode proteins belonging to several functional classes including enzymes, transporters and small secreted proteins. Among them, glycoside hydrolases and transporters are highlighted by their abundance and suggest an important factor in the metabolism of host cell walls during colonization of the outer root layers. Activity of the CBH1 promoter was reported by GFP fluorescence in a transgenic T. virens line on roots, providing a first spatial view of how the plant re-programs the fungal transcriptome. Host-specific gene expression may contribute to the ability of T. virens to colonize the roots of a wide range of plant species. The host-specific gene list obtained here will facilitate functional experiments to test this hypothesis.
Availability of supporting data
The microarray data sets supporting the results of this article are available in the GEO repository, http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=GSE64344.
We are grateful to Michal Levin and Itai Yanai for use of the microarray platform and help with data analysis; Nitsan Dahan for his expert assistance with confocal microscopy, and the microscopy unit of the Life Sciences and Engineering core center (Technion) for use of the confocal and binocular fluorescence microscopes. We thank Gillian Turgeon for plasmid pUCATPH, and Tamar Eviatar-Ribak from Eliezer Lifschitz’ lab for tomato seeds. We are grateful to Judith Horwitz for assistance in managing the gene lists. Doctoral fellowships to N.T and N.L.L. were funded in part by the Irwin and Joan Jacobs Graduate School, Technion. This study was supported by the Texas Department of Agriculture and the US-Israel Binational Agricultural Research and Development Fund (TB-8031-08).
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